GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ald-dh-CoA in Verminephrobacter eiseniae EF01-2

Align alcohol dehydrogenase (EC 1.1.1.1); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_011811972.1 VEIS_RS20705 aldehyde dehydrogenase family protein

Query= BRENDA::Q70YJ9
         (885 letters)



>NCBI__GCF_000015565.1:WP_011811972.1
          Length = 482

 Score =  231 bits (588), Expect = 1e-64
 Identities = 152/462 (32%), Positives = 230/462 (49%), Gaps = 20/462 (4%)

Query: 34  QKSKSDEEGLSSLKSTLNKAVAASKVFATYSQDQVDKIFRAAAEAA--NAARLPLAKMAV 91
           + S +     S +   + +A AA ++ AT+SQ Q D    AA  A    A    LA++AV
Sbjct: 2   EHSTAPSSAPSPITELVARARAAQRICATWSQAQADTAVTAAGWAIIEPARNRELAELAV 61

Query: 92  EETRMGVVEDKVIKNHFASEFVYSQYKNTKTCGLIAHDPISGYSKFAEPMGVIAGIIPTT 151
            +T MG V+DKV+KNH  +  +       ++ G+I  DP  G  + A P+GV+  I P+T
Sbjct: 62  ADTGMGCVQDKVLKNHRKTFGLLRDLHGARSVGVIGQDPARGIVEIARPVGVVCAITPST 121

Query: 152 NPTSTAIFKTLLALKTRNALVICPHPRAAKCTIAAAKVVLDAAVAAGAPADIITWIDSP- 210
           NP +T   K + ALK RNA+V+ P P+           +       GAP D++  +  P 
Sbjct: 122 NPGATPANKIINALKGRNAVVVAPSPKGWSTAARLIGFIHAQFDRIGAPRDLVQLLPGPI 181

Query: 211 SSLVSGALMKAPGSVLVLATGGPGMVRAVTLPA-PSLGVGAGNTPALIDETADIELAVNS 269
               +G LM+     LV+ATG    VRA      P+ GVGAGN   ++DETAD+  A   
Sbjct: 182 DKQATGELMRLCD--LVVATGSQANVRAAYASGTPAFGVGAGNVAGIVDETADVHAAAER 239

Query: 270 VLISKTFDNGVICASEQSIVAVDAVYDKVRAEFVRRGAYFLNEEEKVKVRKGIEKDGKLN 329
           ++ SKTFDN   C+SE S+V VDAV   + A    RGA  L   +K  ++  +   GKL+
Sbjct: 240 IVRSKTFDNATSCSSENSLVIVDAVRAPMLAALAERGAVMLTAAQKATLQALMWPGGKLS 299

Query: 330 ADIVGQPVAKLAQMFGITVPA-----------GAKVLIGEVSVVGKEEPLSQEKLSPILA 378
           A ++GQ    +A+       A           G ++L+      G   P S EKLSP+LA
Sbjct: 300 AAVIGQSARSIAERAAALDDAQCAGWLALAATGPRILMVAEDGAGHGHPFSGEKLSPVLA 359

Query: 379 MYRSSDFNTALATTHKLIMFGGAGHTSVIYTHPDNRQNIEAFQAMAKTGRILVNSPSSQG 438
           ++ + +F  A A   ++    GAGH+  +  H    +            R++V+   S  
Sbjct: 360 IHGAQNFAAAAAMVERIYAHEGAGHS--VGLHSALPERALTLGLTLPVARVIVDQAHSI- 416

Query: 439 AIGGIYNQILAPSMTLGCGSWGGNIVSDNIGPLHLVNVKSVA 480
           A GG ++  L  S+++GCG+WG N  SDN+   H +N+  V+
Sbjct: 417 ATGGSFDNGLPFSLSMGCGTWGKNSFSDNLNYRHYLNITRVS 458


Lambda     K      H
   0.316    0.130    0.360 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 866
Number of extensions: 45
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 885
Length of database: 482
Length adjustment: 38
Effective length of query: 847
Effective length of database: 444
Effective search space:   376068
Effective search space used:   376068
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory